What second patch? You only need to apply one of the 2 patches that come with the RTC Fix.
They're in 2 different formats, so you can choose whichever you want, IPS or UPS. Both make the exact same changes, so you don't need to use both of them.
All you have to do is apply Red Chapter's patch, and then one of the 2 patch files that the RTC Fix is distributed as, IPS or UPS over the patched ROM
ON: I'll take the chance to mention that the latest stable release of mGBA seems to run the ROM of the Beta 15 of Red Chapter, even though it's bigger than a regular 32 MB GBA ROM.
Do keep in mind though, that you may still experience crashes, specially when swapping costumes, so when you reach Celadon City things might get messy as you're forced to swap out costumes there for a few story events.